X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=f9c2c4b70e4b4e168c166cde07897d75af72115b;hb=a064561d8665ee9db217b17cda826fceac90cbbc;hp=978316bf2cc8f118c3aa21cb975531f87477d52b;hpb=58c6b8248851792fa37db90c54d55f419a439cad;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index 978316b..f9c2c4b 100644 --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@ -1,53 +1,37 @@ package jalview.ext.ensembl; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertTrue; + +import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; -import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType; import jalview.io.AppletFormatAdapter; import jalview.io.FastaFile; import jalview.io.FileParse; -import jalview.util.DBRefUtils; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.io.gff.SequenceOntologyLite; import java.lang.reflect.Method; +import java.net.MalformedURLException; +import java.net.URL; import java.util.Arrays; +import java.util.List; import org.testng.Assert; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; + public class EnsemblSeqProxyTest { - @Test - public void testCheckEnsembl() - { - SeqFetcher sf = new SeqFetcher(); - sf.setTestEnsemblStatus(true); - sf.setTesting(true); - Assert.assertTrue(sf.isEnsemblAvailable()); - sf.setTestEnsemblStatus(false); - Assert.assertFalse(sf.isEnsemblAvailable()); - } - - @Test(suiteName = "live") - public void testLiveCheckEnsembl() - { - SeqFetcher sf = new SeqFetcher(); - boolean isAvailable = sf.isEnsemblAvailable(); - System.out.println("Ensembl is " - + (isAvailable ? "UP!" : "DOWN ******************* BAD!")); - } - - @DataProvider(name = "ens_seqs") - public Object[][] createData(Method m) - { - System.out.println(m.getName()); - return allSeqs; - } - - public static Object[][] allSeqs = new Object[][] - { + private static final Object[][] allSeqs = new Object[][] { { - EnsemblSeqType.PROTEIN, + new EnsemblProtein(), "CCDS5863.1", ">CCDS5863.1\n" + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n" @@ -64,7 +48,7 @@ public class EnsemblSeqProxyTest + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n" + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" }, { - EnsemblSeqType.TRANSCRIPT, + new EnsemblCdna(), "CCDS5863.1", ">CCDS5863.1\n" + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n" @@ -107,7 +91,7 @@ public class EnsemblSeqProxyTest + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n" + "GGTGCGTTTCCTGTCCACTGA\n" }, { - EnsemblSeqType.PROTEIN, + new EnsemblProtein(), "ENSP00000288602", ">ENSP00000288602\n" + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n" @@ -124,12 +108,31 @@ public class EnsemblSeqProxyTest + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n" + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } }; + @BeforeClass + public void setUp() + { + SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); + } + + @AfterClass + public void tearDown() + { + SequenceOntologyFactory.setInstance(null); + } + + @DataProvider(name = "ens_seqs") + public Object[][] createData(Method m) + { + System.out.println(m.getName()); + return allSeqs; + } + @Test(dataProvider = "ens_seqs", suiteName = "live") - public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq) + public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq) throws Exception { - SeqFetcher sf = new SeqFetcher(); - FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[] + FileParse fp = proxy.getSequenceReader(Arrays + .asList(new String[] { sq })); SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray(); FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE); @@ -152,48 +155,96 @@ public class EnsemblSeqProxyTest "Sequences differ for " + tr.getName() + "\n" + "Exp:" + tr.getSequenceAsString() + "\n" + "Got:" + rseq[0].getSequenceAsString()); - + } } - @Test(dataProvider = "ens_seqs") - public void testRegexForProxy(EnsemblSeqType type, String sq, - String fastasq) throws Exception + @Test(suiteName = "live") + public void testLiveCheckEnsembl() + { + EnsemblRestClient sf = new EnsemblRestClient() + { + + @Override + public String getDbName() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public AlignmentI getSequenceRecords(String queries) throws Exception + { + // TODO Auto-generated method stub + return null; + } + + @Override + protected URL getUrl(List ids) throws MalformedURLException + { + // TODO Auto-generated method stub + return null; + } + + @Override + protected boolean useGetRequest() + { + // TODO Auto-generated method stub + return false; + } + + @Override + protected String getRequestMimeType(boolean b) + { + // TODO Auto-generated method stub + return null; + } + + @Override + protected String getResponseMimeType() + { + // TODO Auto-generated method stub + return null; + } + + }; + boolean isAvailable = sf.isEnsemblAvailable(); + System.out.println("Ensembl is " + + (isAvailable ? "UP!" + : "DOWN or unreachable ******************* BAD!")); + } + + @Test(groups = "Functional") + public void getGenomicRangesFromFeatures() + { + + } + + @Test(groups = "Functional") + public void testIsTranscriptIdentifier() + { + EnsemblSeqProxy testee = new EnsemblGene(); + assertFalse(testee.isTranscriptIdentifier(null)); + assertFalse(testee.isTranscriptIdentifier("")); + assertFalse(testee.isTranscriptIdentifier("ENSG00000012345")); + assertTrue(testee.isTranscriptIdentifier("ENST00000012345")); + assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345")); + assertFalse(testee.isTranscriptIdentifier("enst00000012345")); + assertFalse(testee.isTranscriptIdentifier("ENST000000123456")); + assertFalse(testee.isTranscriptIdentifier("ENST0000001234")); + } + + @Test(groups = "Functional") + public void testIsGeneIdentifier() { - EnsemblSeqProxy esq = new EnsemblProtein(); - Assert.assertTrue(esq.isValidReference(sq), - "Expected reference string " + sq + " to be valid for regex " - + esq.getAccessionValidator().toString()); - - Assert.assertEquals(sq, DBRefUtils.processQueryToAccessionFor(esq, sq), - "Regex for " + esq.getClass().toString() + " not correct."); + EnsemblSeqProxy testee = new EnsemblGene(); + assertFalse(testee.isGeneIdentifier(null)); + assertFalse(testee.isGeneIdentifier("")); + assertFalse(testee.isGeneIdentifier("ENST00000012345")); + assertTrue(testee.isGeneIdentifier("ENSG00000012345")); + assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345")); + assertFalse(testee.isGeneIdentifier("ensg00000012345")); + assertFalse(testee.isGeneIdentifier("ENSG000000123456")); + assertFalse(testee.isGeneIdentifier("ENSG0000001234")); } - // TODO: - // sequence query with ENSG and anything other than a genomic type will yield - // sequences with different IDs which will - // break the post-processing stage where DBRefs are assigned to sequences. - // -> multiple_sequences = true is needed additional parameter - // http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/x-json;type=protein;multiple_sequences=true - // result with four transcripts, cds, cdna, and protein products. - // * - // features for ENG - - // http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=cds&feature=exon&feature=transcript&content-type=text/x-gff3 - // transcript: gives locus, all transcript products with ENSG parents - // gene: give all ENSG on locus - // exon: all exon boundaries. CDS same info. - - // @Test(dataProvider = "ens_seqs", suiteName = "live") - // public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq) - // throws Exception - // { - // - // { - // Assert.assertTrue(rseq[0].getDBRef() != null - // && rseq[0].getDBRef().length > 0, - // "No database references added to sequence by fetcher."); - // Assert.assertNotNull(DBRefUtils.searchRefs(rseq[0].getDBRef(), - // new DBRefEntry("ENSEMBL", null, sq)), - // "Could't find database references added to sequence by fetcher."); - // - // } } \ No newline at end of file